How can I avoid running out of memory in to3d?
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Q33. How can I avoid running out of memory in to3d?
to3d assembles the new dataset into RAM before writing it to disk in the .BRIK file. As it is reading 2D slices from the input files, it will need to have in memory one input file at a time and also the entire new dataset. If the input file comprises all the new dataset, this means that twice as much RAM is needed during input as is needed to store the new dataset brick(s). (The code was written this way because our image reconstruction software gives us our images as individual slice files. In this case, the overhead is just the amount of memory needed for one slice, which is trivial.)
To avoid this problem, the "-in:1" switch was added to to3d. If you use this, then only one 2D slice will be read out of each input file at a time. When inputting a big 3D or 4D file, this results in somewhat more disk I/O, but saves a lot of memory.
On HP-UX systems, another problem is that HP seems to ship the Unix kernel configured so that each running program can only access 64 MB of RAM, no matter how much the system actually has. To fix this, the super-user (root) has to use the SAM program (part of HP-UX) to adjust the kernel parameters, and then rebuild the operating system. Ugly, but true.
This FAQ applies to: Any version.
